ABySS 1.3.2

ABySS is a de novo sequence assembler that is designed for short reads
and large genomes.

Signed-off-by: Adam Vandenberg <flangy@gmail.com>

1 files changed, 50 insertions, 0 deletions

diff --git a/Library/Formula/abyss.rb b/Library/Formula/abyss.rb
new file mode 100644
index 000000000..cae435580
--- /dev/null
+++ b/Library/Formula/abyss.rb
@@ -0,0 +1,50 @@
+require 'formula'
+
+class Abyss < Formula
+  homepage 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
+  url 'http://www.bcgsc.ca/downloads/abyss/abyss-1.3.2.tar.gz'
+  md5 'a7551c95f33a0c61cab50bc35db347e4'
+
+  # Only header files are used from these packages, so :build is appropriate
+  depends_on 'boost' => :build
+  depends_on 'google-sparsehash' => :build
+
+  # Snow Leopard comes with mpi but Lion does not
+  depends_on 'open-mpi' if MacOS.lion?
+
+  # strip breaks the ability to read compressed files.
+  skip_clean 'bin'
+
+  # abyss-overlap does not build with LLVM-GCC, so skip it. See:
+  # http://lists.apple.com/archives/xcode-users/2011/Oct/msg00241.html
+  # https://github.com/mxcl/homebrew/pull/10550
+  def patches
+    DATA
+  end
+
+  def install
+    system "./configure", "--disable-dependency-tracking",
+                          "--prefix=#{prefix}"
+    system "make install"
+  end
+
+  def test
+    system "#{bin}/ABYSS --version"
+  end
+end
+
+__END__
+diff --git a/Map/Makefile.in b/Map/Makefile.in
+index 7a4e5a8..4dd5dd5 100644
+--- a/Map/Makefile.in
++++ b/Map/Makefile.in
+@@ -32,8 +32,7 @@ POST_INSTALL = :
+ NORMAL_UNINSTALL = :
+ PRE_UNINSTALL = :
+ POST_UNINSTALL = :
+-bin_PROGRAMS = abyss-index$(EXEEXT) abyss-map$(EXEEXT) \
+-	abyss-overlap$(EXEEXT)
++bin_PROGRAMS = abyss-index$(EXEEXT) abyss-map$(EXEEXT)
+ subdir = Map
+ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ ACLOCAL_M4 = $(top_srcdir)/aclocal.m4